Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5478 |
| PDBID: | 7WTK |
| Chains: | IK_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.60 |
| Reference: | 10.1038/s41422-022-00677-z |
| Antibody | |
| Antibody: | XGv286 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7WTK_I|Chain B[auth G], F[auth H], G[auth I]|Heavy chain of XGv286|Homo sapiens (9606) VQLVQSGAEVKKPGASVKVSCKASGYTFSSYYIHWVRQAPGQGPEWMAIINPGDGGASYAQKFQGRVTLTRDTSTSTLYMELSSLRSEDTAVYYCARAEGSSWLGWFDPWGQGTLVTV |
Light Chain: K
Mutation: NULL
| >7WTK_K|Chain C[auth J], H[auth K], I[auth L]|Light chain of XGv286|Homo sapiens (9606) SVLTQPPSASGTPGQRVTISCSGSSSNIGSNYVYWYQQLPGTAPKLLIYRNNQRPSGVPDRFSGSRSGTSASLAISGLRSEDEADYYCAAWDDGLSGSGWVFGGGTKLT |
Antigen
Chain: A
Mutation: A54V/A80I/F127D/193I/G323D/S355L/S357P/S359F/K401N/N424K/G430S/S461N/T462K/E468A/Q477R/G480S/Q482R/N485Y/Y489H/T531K/D598G/H639Y/R667A/R669A/N748K/D780Y/F801P/N840K/A876P/A883P/A926P/Q938H/N953K/L965F/K970P/V971P
| >7WTK_A|Chain A, D[auth B], E[auth C]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTNSPRAAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPRRA |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| I: TYR33 TRP47 ILE50 ASN52 ASP55 GLY57 ALA58 SER59 TYR60 ALA61 GLN65 SER102 TRP104 LEU105 K: SER31 ASN32 TRP92 ASP94 GLY95 LEU96 SER97 GLY98 SER99 A: ALA374 PRO375 ASN439 ASN441 LYS442 LYS446 VAL447 SER448 ARG500 PRO501 THR502 TYR503 GLY504 VAL505 HIS507 GLN508 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
